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Champion bosses come with more drastic differences:
Aside from increased damage, some might even posses new abilities (the champion Larry Jr. gaining the ability to spit shots, for example) or are otherwise more threatening (Monstro might appear with a duplicate, and Peep can start with both eyes removed). Faster movement (like Gemini) is also common, or a change in spawning behavior (Gurdy might just spawn instead of shooting, and Chub might also spawn Spities or Boils instead of Chargers).

Champion forms of bosses will always drop a heart upon defeat when found outside a boss room or an extra heart when found inside a boss room. If the champion boss is blue, the heart(s) dropped will instead be a Soul Heart.

Dark Red - when killed it leaves behind goo. If the goo is not killed the champion revives, like a globin. Drops a double heart. Works with certain suicide moves, like Mulligan self-exploding, but doesn't stack with Globin native ability.

Pink - randomly shoots a projectile in the direction it is facing. Drops nothing

Yellow - moves considerably faster. Drops Lil Battery

Grey - has decreased health. Drops key.

Dark Grey - explodes after death. Drops a bomb.

Light Blue - shoots eight projectiles upon death. Drops 1/2 heart

Dark Blue - gives three blue flies after death

Gold - steals money from you when it hurts you. Drops a coin.

Black - randomly turns invisible. Drops a red chest.

Purple - pulls in you and your shots. Drops a random trinket.

Transparent - can move over any object. Drops a golden chest.

White: is invincible until everything in the room is killed. Drops an eternal heart

Some colors can be distorted, since champion color mixes with common enemy color.

A lot of new champion bosses were added in the v1.4 update, including champion forms of bosses that previously did not have one. This includes all Wrath of the Lamb bosses as well as bosses from the basic game, like The Harbingers or even Mom.

Champion versions of enemies could be a reference to Diablo II, which has champion enemies that have different colors, and do more damage.